#!/usr/bin/python
import os

basename = "btsnpSNP_6-chr"
mapfilename = basename + ".map"
pedfilename = basename + ".ped"

os.system("plink --ped " + pedfilename + " --map " + mapfilename + " --map3 --missing-genotype 0 --1 --out " + basename + " --make-bed")
os.system("plink --bfile " + basename + " --check-sex --out " + basename)
#os.system("plink --bfile " + basename + " --mind 0.1 --maf 0.05 --hwe 0.00001 --make-bed --out " + basename+"_cleaned")
#os.system("plink --bfile data --keep {indlist})  #Keep only these individuals
#os.system("plink --bfile " + basename + " --assoc --1 --out " + basename)
#os.system("plink --bfile " + basename + "_cleaned " + " --model --model-trend --out " + basename + "_model_trend")
